There are so many games in the franchise but I know only a handful of them are iconic and great and some of them are Ultima 9 level of bad.

Like which were the true classics and worthy of being played now, and which are the bad ones that cause grief and sadness?

Well over 10 years on, Me and the misses will still play RA2+Yuri's Revenge in co-op. A Couple of times a year, for a few weeks we'll make our way through the co-op campaigns. So for us RA2 will always be the best.

C+C4 was horrible. Any RTS game which you can go AFK for an hour and return with your base intact has been reduced below lowest base level.

Didn't like how RA3 forced you to have an AI commander when played Single player.

3 is when the DRM kicked in so I pick that one.

It's the multiplayer component that they wanted to accentuate that killed it I think, and that I believe started with Red Alert 3 and its cooperative-minded design. But it was still a good and fun game, though less so for me than C&C3. However, C&C4 completely binned the series it seems. So I'd say Red Alert 3 marks the start of the decline.
Possible DRM issues aside, I think that C&C3 was a bloody awesome C&C game. I massively enjoyed its campaign. But I might give RA3 a pass nonetheless, simply because of Gemma Atkinson :D

What I really want though is not a new C&C, but a new Dune RTS, complete with cheesy FMVs and all

As for which are the classics and still worth playing today? That's difficult for me to answer due to a big nostalgia factor. The original is still fun, but don't expect the kind of mission variety like in Starcraft or later Blizzard titles. A simple tank rush strategy is sufficient for almost all levels, but there is room for some more clever strategies, some way more effective than simple tank rushes.
Red Alert will perhaps be a bit easier to play from this point of view. There are interesting indoor levels for example, though otherwise mechanically both games are very similar. Dune 2000 is also a pretty good classic, with an engine slightly more advanced than the one used for Red Alert. I especially like it due to it's cool atmosphere (Emperor is also very good, but it's gameplay takes some getting used to).
Everything after this point still holds up very well today: Tiberian Sun, Red Alert 2, Generals, C&C3 + expansion for each.

Personally I wouldn't start with anything later than Tiberian Sun. It's far too awesome to miss with a really cool cyberpunk post-apocalyptic vibe unmatched by anything else in the genre.

Red Alert 3. Up to and Command and Conquer 3, it was still alive and good. As long as Westwood had been around, the legend was real and alive. EA took over and shitstorm paints everything in little brown jelly-beans! Anything EA touches, is being transmuted from GOLD, to SHIT!

Even worse, they spend not a single dime or working-hour, in making games compatible with modern systems. The best games in the series, like RA2 and Yuri's, are actually completely unplayable (and don't even mention the fan overhaul with multi support, it is broken because players themselves arbitrarily chop-off game content by self-imposed restrictions and "rules").

Actually, C&C would have been the best thing to ever come at GOG. All it needs is removal of DRM and tweaking to run as it properly should.

I have to agree here, RA3 is where C&C started to go to shit, it would be a couple of years later that we would get the franchise killer C&C 4.

If C&C, TS and RA 1 to 2 and C&C 3 where to come to GOG, I would be quite happy.

I'd say the last one, C&C 4, which killed the series. I liked C&C Generals, Tiberium Wars and RA3 so it didn't start with the closure of Westwood IMO.

EA started the decline.

Is Jon Van Canegham still the head of C&C at EA? Someone save that poor man and get him back to making amazing Might and Magic games.

I agree that everything before CC4 is golden, including RA3.

I bet pre-CC3 games are never going to make it here simply because of technical problems. Making them reliably run on modern-day OS would require a significant overhaul of the graphics engine, it's not a matter of flipping a few compatibility flags. Whoever may have the rights to the code, they are not going to hire any developers to do it, and that's assuming the source code is still around.

I'd say right after Red Alert 2. I enjoy Generals very much, but the thing is that Generals doesn't look like a C&C game (even the UI is completely different than the previous games) and doesn't have that atmosphere the previous games had; it changed a lot on that account, to the point that i usually see it as a spin-off to the franchise. They even discontinued the FMVs that were kinda like a trademark of the series and personally i couldn't get enough of them (Yuri FTW!).

My favourites of the series are Red Alert, Red Alert 2 & Tiberian Sun.

ps. If you haven't done it already, check out OpenRA. ;)

I don't think I'd hate #3 so much if I could get the fucking thing to run on my computer. :P

WTF is "Exception in Exception Handler" anyway? :P

C&C 3 is ok but nowhere near the classics. Red Alert 3 was meh. C&C4 was downright horrible, not even the awesome Joe Kucan could save it.

The Red Alert games are one of my favorite C&C games, after those I was always disappointed in what was released.

I thought it was fairly self-explanatory, it's an exception in a handler than handles exceptions.